Project ID ::: CTR_kf284_0002
Centre for Trophoblast Research, University of Cambridge
Created by CTR Bioinformatics
- Analysis by:
- Russell S. Hamilton
- Contact E-mail:
- rsh46@cam.ac.uk
- Application Type:
- RNA-seq
- Project Type:
- RNA-Seq Quality Control
- Project Owners:
- Damiano Giuseppe Barone / Kristian Franze
- Sequencing Platform:
- Illumina
- Sequencing Setup:
- SE 50bp
Report generated on 2017-11-22, 15:11 based on data in:
/rds/project/rsh46/rds-rsh46-ctr-bfx/CTR-Projects/CTR_kf284_0002
General Statistics
Showing 1310 samples.
QualiMap
QualiMap is a platform-independent application to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.
Genomic origin of reads
Gene Coverage Profile
Cutadapt
Cutadapt is a tool to find and remove adapter sequences, primers, poly-Atails and other types of unwanted sequence from your high-throughput sequencing reads.
This plot shows the number of reads with certain lengths of adapter trimmed. Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length. See the cutadapt documentation for more information on how these numbers are generated.
FastQ Screen
FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.
Summed alignment percentages are shown below. Note that percentages can sum to greater than 100% if reads align to multiple organisms.
FastQC
FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.
Sequence Quality Histograms
The mean quality value across each base position in the read. See the FastQC help.
Per Sequence Quality Scores
The number of reads with average quality scores. Shows if a subset of reads has poor quality. See the FastQC help.
Per Base Sequence Content
The proportion of each base position for which each of the four normal DNA bases has been called. See the FastQC help.
Click a heatmap row to see a line plot for that dataset.
rollover for sample name
Per Sequence GC Content
The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content. See the FastQC help.
Per Base N Content
The percentage of base calls at each position for which an N was called. See the FastQC help.
Sequence Length Distribution
The distribution of fragment sizes (read lengths) found. See the FastQC help.
Sequence Duplication Levels
The relative level of duplication found for every sequence. See the FastQC help.
Adapter Content
The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. See the FastQC help. Only samples with ≥ 0.1% adapter contamination are shown.
